Protein Drug Development Research Articles

MetaDegron: multimodal feature-integrated protein language model for predicting E3 ligase targeted degrons.

Protein degradation through the ubiquitin proteasome system at the spatial and temporal regulation is essential for many cellular processes. E3 ligases and degradation signals (degrons), the sequences they recognize in the target proteins, are key parts of the ubiquitin-mediated proteolysis, and their interactions determine the degradation specificity and maintain cellular homeostasis. To date, only a limited number of targeted degron instances have been identified, and their properties are not yet fully characterized. To tackle on this challenge, here we develop a novel deep-learning framework, namely MetaDegron, for predicting E3 ligase targeted degron by integrating the protein language model and comprehensive featurization strategies. Through extensive evaluations using benchmark datasets and comparison with existing method, such as Degpred, we demonstrate the superior performance of MetaDegron. Among functional features, MetaDegron allows batch prediction of targeted degrons of 21 E3 ligases, and provides functional annotations and visualization of multiple degron-related structural and physicochemical features. MetaDegron is freely available at http://modinfor.com/MetaDegron/. We anticipate that MetaDegron will serve as a useful tool for the clinical and translational community to elucidate the mechanisms of regulation of protein homeostasis, cancer research, and drug development.

The application of nanodiscs in membrane protein drug discovery & development and drug delivery.

The phospholipid bilayer nanodiscs (LNDs), as a rapidly-developing tool in recent years, provide a natural bio-memebrane environment to maintain the native conformation and functions of membrane proteins as well as a versatile delivery vehicle for a variety of hydrophobic and hydrophilic drugs. We have seen unprecedented advantages of phospholipid bilayer nanodiscs in membrane protein structure characterization, biochemical and physiological studies of membrane proteins, membrane environment studies, drug discovery & development, and drug delivery. Many previous reviews have been mainly focused on the advantages of nanodiscs in membrane protein researches, but few have touched upon the importance and potential application of nanodiscs in pharmaceutical industries. This review will provide general description of the structural characteristics, advantages, classification, and applications of phospholipid nanodiscs, with particular focus on nanodisc-enabled membrane protein drug discovery & development as well as drug delivery.

Efficient cytosolic delivery of proteins enabled by modular fusion protein

The development of protein-based biotechnology and drugs holds tremendous potential for various applications. However, the effective intracellular delivery of natural proteins remains a challenge due to their inability to spontaneously penetrate the cell membrane. In this study, we have developed a modular fusion protein sequence that overcomes this limitation and enables efficient cytoplasmic protein delivery . This modular fusion protein we designed has demonstrated efficient lysosomal escape ability, allowing for successful delivery of various protein cargoes into the cytoplasm of different cell types. Importantly, the fusion with the mCherry tag does not affect the biological activity of the protein. The fusion protein can still exert its catalytic activity when delivered into cells. We also designed a fluorescent protein probe capable of precisely targeting lysosomes, providing powerful fluorescent probe tools for intracellular localization and tracking in biomedical research. This approach contributes to the advancement of protein drug development and opens up new possibilities for therapeutic interventions.

DeepPLM_mCNN: An approach for enhancing ion channel and ion transporter recognition by multi-window CNN based on features from pre-trained language models

Accurate classification of membrane proteins like ion channels and transporters is critical for elucidating cellular processes and drug development. We present DeepPLM_mCNN, a novel framework combining Pretrained Language Models (PLMs) and multi-window convolutional neural networks (mCNNs) for effective classification of membrane proteins into ion channels and ion transporters. Our approach extracts informative features from protein sequences by utilizing various PLMs, including TAPE, ProtT5_XL_U50, ESM-1b, ESM-2_480, and ESM-2_1280. These PLM-derived features are then input into a mCNN architecture to learn conserved motifs important for classification. When evaluated on ion transporters, our best performing model utilizing ProtT5 achieved 90% sensitivity, 95.8% specificity, and 95.4% overall accuracy. For ion channels, we obtained 88.3% sensitivity, 95.7% specificity, and 95.2% overall accuracy using ESM-1b features. Our proposed DeepPLM_mCNN framework demonstrates significant improvements over previous methods on unseen test data. This study illustrates the potential of combining PLMs and deep learning for accurate computational identification of membrane proteins from sequence data alone. Our findings have important implications for membrane protein research and drug development targeting ion channels and transporters. The data and source codes in this study are publicly available at the following link: https://github.com/s1129108/DeepPLM_mCNN.

Personalized Drug Therapy: Innovative Concept Guided With Proteoformics

Personalized medicine can reduce adverse effects, enhance drug efficacy, and optimize treatment outcomes, which represents the essence of personalized medicine in the pharmacy field. Protein drugs are crucial in the field of personalized drug therapy and are currently the mainstay, which possess higher target specificity and biological activity than small-molecule chemical drugs, making them efficient in regulating disease-related biological processes, and have significant potential in the development of personalized drugs. Currently, protein drugs are designed and developed for specific protein targets based on patient-specific protein data. However, due to the rapid development of two-dimensional gel electrophoresis and mass spectrometry, it is now widely recognized that a canonical protein actually includes multiple proteoforms, and the differences between these proteoforms will result in varying responses to drugs. The variation in the effects of different proteoforms can be significant and the impact can even alter the intended benefit of a drug, potentially making it harmful instead of lifesaving. As a result, we propose that protein drugs should shift from being targeted through the lens of protein (proteomics) to being targeted through the lens of proteoform (proteoformics). This will enable the development of personalized protein drugs that are better equipped to meet patients' specific needs and disease characteristics. With further development in the field of proteoformics, individualized drug therapy, especially personalized protein drugs aimed at proteoforms as a drug target, will improve the understanding of disease mechanisms, discovery of new drug targets and signaling pathways, provide a theoretical basis for the development of new drugs, aid doctors in conducting health risk assessments and making more cost-effective targeted prevention strategies conducted by artificial intelligence/machine learning, promote technological innovation, and provide more convenient treatment tailored to individualized patient profile, which will benefit the affected individuals and society at large.

Significance of genetic code module structure in gene expression and GC content enhancement in RNA sequences

The existent algebraic models of the genetic code contribute to the understanding of the physio-chemical characteristics of the amino acids. However, the process of translating a gene into a phenotype is highly complex. Moreover, the intricacy of gene expression gets further multiplied due to the biases in the codon usage. This paper explores an algebraic structure called module on the set of codons as well as on that of RNA sequences. We study the potential implications of these structures on gene expression and the GC content of an RNA sequence. The base order {C,U,G,A} appears to possess greater biological significance than many of the orders previously studied. We have developed a novel algorithm to generate RNA sequences with high GC content, aiming to enhance the thermostability of biomolecules. The insights gained from this investigation may have applications in biomolecular modeling and docking, protein engineering, drug development, and related fields.

Current Challenges and Approaches on Delivery of Protein Based Formulations

Numerous obstacle crops up in the path of developing efficient protein-based formulations and administration in humans for their therapeutic effect. The challenges starts from protein synthesis to it’s handling procedure, stability, storage, excipients compatibility, scale up, analysis, validation, tissue targeting, in-vivo bioavailability, immunogenic reactions, etc., In the field of protein drug development, various novel methods and techniques have been evolved and continuing the research to face those challenges to bring out potential drug formulations and its delivery system to the market. It is vital to develop various strategies for protecting the integrity of proteins, increasing their availability in the body, decreasing immunological responses, transporting and target to particular tissues or cells. This current review focuses on to understand the problems, challenges encountering and the best approaches for protein based drug formulation development. It is one of roadmap to plan various research activities for continual improvement of therapeutic applications of newly developing protein drugs in this area.

Correlation of In Vitro Kinetic Stability to Preclinical In Vivo Pharmacokinetics for a Panel of Anti-PD-1 Monoclonal Antibody Interleukin 21 Mutein Immunocytokines.

The development of therapeutic fusion protein drugs is often impeded by the unintended consequences that occur from fusing together domains from independent naturally occurring proteins, consequences such as altered biodistribution, tissue uptake, or rapid clearance and potential immunogenicity. For therapeutic fusion proteins containing globular domains, we hypothesized that aberrant in vivo behavior could be related to low kinetic stability of these domains leading to local unfolding and susceptibility to partial proteolysis and/or salvage and uptake. Herein we describe an assay to measure kinetic stability of therapeutic fusion proteins by way of their sensitivity to the protease thermolysin. The results indicate that in vivo pharmacokinetics of a panel of anti-programmed cell death protein 1 monocolonal antibody:interleukin 21 immunocytokines in both mice and nonhuman primates are highly correlated with their in vitro susceptibility to thermolysin-mediated proteolysis. This assay can be used as a tool to quickly identify in vivo liabilities of globular domains of therapeutic proteins, thus aiding in the optimization and development of new multispecific drug candidates. SIGNIFICANCE STATEMENT: This work describes a novel assay utilizing protein kinetic stability to identify preclinical in vivo pharmacokinetic liabilities of multispecific therapeutic fusion proteins. This provides an efficient, inexpensive method to ascertain inherent protein stability in vitro before conducting in vivo studies, which can rapidly increase the speed of preclinical drug development.

PoSSuM v.3: A Major Expansion of the PoSSuM Database for Finding Similar Binding Sites of Proteins.

Information on structures of protein-ligand complexes, including comparisons of known and putative protein-ligand-binding pockets, is valuable for protein annotation and drug discovery and development. To facilitate biomedical and pharmaceutical research, we developed PoSSuM (https://possum.cbrc.pj.aist.go.jp/PoSSuM/), a database for identifying similar binding pockets in proteins. The current PoSSuM database includes 191 million similar pairs among almost 10 million identified pockets. PoSSuM drug search (PoSSuMds) is a resource for investigating ligand and receptor diversity among a set of pockets that can bind to an approved drug compound. The enhanced PoSSuMds covers pockets associated with both approved drugs and drug candidates in clinical trials from the latest release of ChEMBL. Additionally, we developed two new databases: PoSSuMAg for investigating antibody-antigen interactions and PoSSuMAF to simplify exploring putative pockets in AlphaFold human protein models.

Applications of genetic code expansion technology in eukaryotes.

Unnatural amino acids (UAAs) have gained significant attention in protein engineering and drug development owing to their ability to introduce new chemical functionalities to proteins. In eukaryotes, genetic code expansion (GCE) enables the incorporation of UAAs and facilitates posttranscriptional modification (PTM), which is not feasible in prokaryotic systems. GCE is also a powerful tool for cell or animal imaging, the monitoring of protein interactions in target cells, drug development, and switch regulation. Therefore, there is keen interest in utilizing GCE in eukaryotic systems. This review provides an overview of the application of GCE in eukaryotic systems and discusses current challenges that need to be addressed.

Lipid-Based Nanoparticles as Oral Drug Delivery Systems: Overcoming Poor Gastrointestinal Absorption and Enhancing Bioavailability of Peptide and Protein Therapeutics.

Delivery and formulation of oral peptide and protein therapeutics have always been a challenge for the pharmaceutical industry. The oral bioavailability of peptide and protein therapeutics mainly relies on their gastrointestinal solubility and permeability which are affected by their poor membrane penetration, high molecular weight and proteolytic (chemical and enzymatic) degradation resulting in limited delivery and therapeutic efficacy. The present review article highlights the challenges and limitations of oral delivery of peptide and protein therapeutics focusing on the application, potential and importance of solid lipid nanoparticles (SLNs) and nanostructured lipid carriers (NLCs) as lipid-based drug delivery systems (LBDDSs) and their advantages and drawbacks. LBDDSs, due to their lipid-based matrix can encapsulate both lipophilic and hydrophilic drugs, and by reducing the first-pass effect and avoiding proteolytic degradation offer improved drug stability, dissolution rate, absorption, bioavailability and controlled drug release. Furthermore, their small size, high surface area and surface modification increase their mucosal adhesion, tissue-targeted distribution, physiological function and half-life. Properties such as simple preparation, high-scale manufacturing, biodegradability, biocompatibility, prolonged half-life, lower toxicity, lower adverse effects, lipid-based structure, higher drug encapsulation rate and various drug release profile compared to other similar carrier systems makes LBDDSs a promising drug delivery system (DDS). Nevertheless, undesired physicochemical features of peptide and protein drug development and discovery such as plasma stability, membrane permeability and circulation half-life remain a serious challenge which should be addressed in future.

Tannic acid-based sustained-release system for protein drugs

In recent years, protein drug development has gained momentum, and simple and facile controlled-release systems without loss of activity are required. Herein, we developed a sustained-release system for protein drugs by exploiting the “astringency” mechanism, namely insoluble precipitate formation by interacting with tannic acid. Tannic acid formed insoluble precipitates with various protein drugs, such as nisin, insulin, lysozyme, ovalbumin, hyaluronidase, and human immunoglobulin G, through hydrophobic interactions and hydrogen bonds. The lysozyme/tannic acid complex retained in vitro lytic activity. Precipitates of the insulin/tannic acid complex prolonged hypoglycemic effects without loss of activity after subcutaneous administration. The ovalbumin/tannic acid complex enhanced anti-ovalbumin antibody production induced by ovalbumin, which may be attributed to its sustained-release profile. Accordingly, tannic acid is useful as a simple and user-friendly drug delivery system for protein drugs.

Unstructured Polypeptides as a Versatile Drug Delivery Technology.

Although polyethylene glycol (PEG), or "PEGylation" has become a widely applied approach for improving the efficiency of drug delivery, the immunogenicity and non-biodegradability of this synthetic polymer have prompted an evident need for alternatives. To overcome these caveats and to mimic PEG -or other natural or synthetic polymers- for the purpose of drug half-life extension, unstructured polypeptides are designed. Due to their tunable length, biodegradability, low immunogenicity and easy production, unstructured polypeptides have the potential to replace PEG as the preferred technology for therapeutic protein/peptide delivery. This review provides an overview of the evolution of unstructured polypeptides, starting from natural polypeptides to engineered polypeptides and discusses their characteristics. Then, it is described that unstructured polypeptides have been successfully applied to numerous drugs, including peptides, proteins, antibody fragments, and nanocarriers, for half-life extension. Innovative applications of unstructured peptides as releasable masks, multimolecular adaptors and intracellular delivery carriers are also discussed. Finally, challenges and future perspectives of this promising field are briefly presented. STATEMENT OF SIGNIFICANCE: : Polypeptide fusion technology simulating PEGylation has become an important topic for the development of long-circulating peptide or protein drugs without reduced activity, complex processes, and kidney injury caused by PEG modification. Here we provide a detailed and in-depth review of the recent advances in unstructured polypeptides. In addition to the application of enhanced pharmacokinetic performance, emphasis is placed on polypeptides as scaffolders for the delivery of multiple drugs, and on the preparation of reasonably designed polypeptides to manipulate the performance of proteins and peptides. This review will provide insight into future application of polypeptides in peptide or protein drug development and the design of novel functional polypeptides.

Global Analysis of Aggregation Profiles of Three Kinds of Immuno-Oncology mAb Drug Products Using Flow Cytometry.

Accurately quantifying the protein particles in both subvisible (1-100 μm) and submicron (≤1 μm) ranges remains a prominent challenge in the development and manufacturing of protein drugs. Due to the limitation of the sensitivity, resolution, or quantification level of various measurement systems, some instruments may not provide count information, while others can only count particles in a limited size range. Moreover, the reported concentrations of protein particles commonly have significant discrepancies owing to different methodological dynamic ranges and the detection efficiency of these analytical tools. Therefore, it is extremely difficult to accurately and comparably quantify protein particles within the desired size range at one time. To develop an efficient protein aggregation measurement method that can span the entire range of interest, we established, in this study, a single particle-sizing/counting method based on our highly sensitive lab-built flow cytometry (FCM) system. The performance of this method was assessed, and its capability of identifying and counting microspheres between 0.2 and 25 μm was demonstrated. It was also used to characterize and quantify both subvisible and submicron particles in three kinds of top-selling immuno-oncology antibody drugs and their lab-produced counterparts. These assessment and measurement results suggest that there may be a role for an enhanced FCM system as an efficient investigative tool for characterizing and learning the molecular aggregation behavior, stability, or safety risk of protein products.

Genome-wide nonessential gene identification of Autographa californica multiple nucleopolyhedrovirus

The Baculovirus Expression Vector System (BEVS) is an insect cell-based heterologous protein expression system that possesses powerful potential in the development of protein drugs and vaccines. Autographa californica multiple nucleopolyhedrovirus (AcMNPV) is the most widely-used vector in BEVS with 151 open reading frames (ORFs) containing essential and nonessential genes. Deletion of nonessential genes has many advantages including increased foreign gene insertion. In this study, the λ red recombination system was used to knock out genes in a modified AcMNPV that carried an enhanced yellow fluorescent protein (eYFP) at the Ac126-Ac127 locus. Eighty genes were almost completely deleted respectively and 69 gene knockout AcMNPVs (KOVs) were obtained to evaluate their infection efficiency. After infecting Spodoptera frugiperda 9 (Sf9) cells, 51 KOVs including 62 genes showed similar infectivity as wide type (WT) and hence were defined as nonessential genes. However, 18 KOVs produced fewer infectious virions, indicating that these genes were influential in the production of progeny viruses. Combining our research with previous studies, a desired minimal AcMNPV genome containing 86 ORFs and all of the homologous regions (hrs) was brought up, facilitating genetic modification of baculovirus vectors and improvement of recombinant protein expression in the future.

A novel aptamer beacon for rapid screening of recombinant cells and in vivo monitoring of recombinant proteins

Recombinant protein drugs, which are typically produced by mammalian host cells, have been approved for the treatment of a range of diseases. Accordingly, systems for selecting recombinant cell lines with efficient protein expression and for testing the content of recombinant proteins in vivo are crucial to the large-scale production and application of protein-based therapeutic drugs. In this study, we designed three aptamer beacons to detect His-tag, a common label of recombinant proteins. We found that all three beacons could specifically and quantitatively measure the His-tagged recombinant proteins with a short reaction time. Among these three beacons, the 6H5-MU beacon had the highest sensitivity for His polypeptides with a detection limit of 250ng/mL and the shortest detection time within 1min. Furthermore, we established a rapid and highly effective recombinant cell line construction system, which could obtain monoclonal cell lines with high yields of target proteins within 21days, by combining 6H5-MU with pSB, a novel plasmid composed of a Sleeping Beauty transposase and a transposon. Finally, 6H5-MU also discriminately tested the serum concentration of His-tagged recombinant proteins in vivo, with consistent results compared to enzyme-linked immunosorbent assay (ELISA). We thus established a rapid and high-throughput method for generating recombinant cell lines and in vivo monitoring of recombinant protein levels, thereby providing a new platform for the development and preparation of recombinant protein drugs. KEY POINTS: • The 6H5-MU aptamer beacon rapidly and accurately binds to His-tagged recombinant proteins. • A system for rapid and high-throughput generation of recombinant cell lines is established using 6H5-MU and pSB. • 6H5-MU allows in vivo monitoring of recombinant protein levels.

Oral Administration of Mice with Cell Extracts of Recombinant Lactococcus lactis IL1403 Expressing Mouse Receptor Activator of NF-kB Ligand (RANKL).

Receptor activator of NF-kB ligand (RANKL) is known to play a major role in bone metabolism and the immune system, and its recombinant form has been expressed in bacterial systems for research since the last two decades. However, most of these recombinant forms are used after purification or directly using living cells. Here, there were cell extracts of recombinant Lactococcus lactis expressing mouse RANKL (mRANKL) used to evaluate its biological activity in mice. Mice were divided into three groups that were fed phosphate-buffered saline (PBS), wild-type L. lactis IL1403 (WT_CE), and recombinant L. lactis expressing mRANKL (mRANKL_CE). The small intestinal transcriptome and fecal microbiome were then profiled. The biological activity of mRANKL_CE was confirmed by studying RANK-RANKL signaling in vitro and in vivo. For small intestinal transcriptome, differentially expressed genes (DEGs) were identified in the mRANKL_CE group, and no DEGs were found in the WT_CE group. In the PBS vs. mRANKL_CE gene enrichment analysis, upregulated genes were enriched for heat shock protein binding, regulation of bone resorption, and calcium ion binding. In the gut microbiome analysis, there were no critical changes among the three groups. However, Lactobacillus and Sphingomonas were more abundant in the mRANKL_CE group than in the other two groups. Our results indicate that cell extracts of mRANKL_CE can play an effective role without a significant impact on the intestine. This strategy may be useful for the development of protein drugs.

Protein Drugs

Abstract: To serve health care, up to now, sciences have successfully developed many drugs with different effects. In general, in terms of chemical structure and effect characteristics, medicine can be classified into groups including inorganic drugs, small-molecule organic drugs, protein drugs (macromolecules), and recently a new group of drugs has been formed, separate from the protein drug class, which is the RNA drugs. In terms of pharmacological effects, in general, the mechanisms of protein drugs and small-molecule organic drugs do not differ too much because they all act at a particular stage related to pathological manifestations.
 Protein drugs in the process of development have gone through many different stages, with different origins, from extraction and isolation from living tissues at an early stage to biosynthesis by recombinant technology and other modern biotechnology methods. To date, most of the proteins used in medicine have been produced through recombinant pathways, possibly through different semisynthetic steps to give the molecules more superior drug properties. Therefore, the group of protein drugs has an additional new name, biopharmaceuticals, to indicate their synthetic origin by biological methods.
 The research, development, and application of protein drugs into clinical practice are of great significance, helping to enhance the ability of medicine to control and treat many difficult-to-treat diseases today, bringing many opportunities to have good health for people.
 Keywords: Protein drugs, RNA drugs, Biopharmaceuticals, Inorganic drugs, Small-molecule organic drugs, Drug development, Cytokine, Enzyme, Hormone peptide, Stem cell, Recombinant technology, Biosimilar. *
 

Nonspecific adsorption evaluation and general minimization strategy in peptide analysis based on ultra-performance liquid chromatography-mass spectrometry

蛋白质组学技术在多肽和蛋白质类新型治疗药物的开发、临床诊断生物标志物的深入发掘中应用广泛。然而,多肽和蛋白质类大分子的非特异性吸附性质给分析方法的开发带来极大挑战,亟须一种通用型的策略去评估和降低非特异吸附对超高效液相色谱-质谱(UPLC-MS)大分子检测造成的负面影响。研究以牛血清白蛋白(BSA)为模型,探讨其酶解后多肽组理化性质与吸附程度之间的相关性;根据肽段的响应和吸附程度设计分级策略;针对高响应、强吸附的Class Ⅱ类肽段,从样品制备中离心管、进样瓶的选择,乃至液相色谱系统中色谱柱固定相、流速、梯度、柱温、洗针液的选择全过程设计试验,探讨非特异吸附的影响因素及其通用型最小化策略。结果显示,肽段的被吸附程度与其理化参数HPLC指数(HPLC Index)、肽段长度等显著相关(p<0.05),但仅凭上述参数仅能解释30%肽段的被吸附程度。改性的聚丙烯材料可使肽段溶液在储存或前处理过程中获得较高的回收率(24 h内回收率大于80%)。在对液相色谱条件的考察和优化过程中发现,C8填料的色谱柱、高流速、缓梯度以及强洗针液,可使残留量降至最低(降低为原来的1/150)。柱温对残留的影响在肽段间存在较大个体差异,需要对不同的肽段具体分析以得到较少量的残留。研究以详实的数据考察并最小化模型肽段组在分析过程中的非特异吸附,提示了蛋白质类大分子药物分析方法建立中应重点关注的影响因素及其有效的解决方案。

Preparation and Characterization of Site-Specific Fatty Chain-Modified Recombinant Human Granulocyte Colony Stimulating Factor.

The clinical use of recombinant human granulocyte colony-stimulating factor (rhG-CSF) is limited by its short serum half-life. In this study, a long-acting strategy for site-specific modification of rhG-CSF with 1-pentadecyl-1H-pyrrole-2,5-dione (C15 fatty chain-maleimide, C15-MAL) was studied in mixed DMSO-aqueous solutions. The factors influencing the conjugation reaction were investigated and optimized, and a high yield of the desired product (C15-rhG-CSF) was achieved. Subsequently, C15-rhG-CSF product was efficiently purified using preparative liquid chromatography, and further characterized. Circular dichroism spectroscopy analysis showed that the secondary structure of C15-rhG-CSF had no significant difference from unmodified rhG-CSF. C15-rhG-CSF retained 87.2% of in vitro bioactivity of unmodified rhG-CSF. The pharmacokinetic study showed that the serum half-life of C15-rhG-CSF in mice was 2.08-fold longer than that of unmodified rhG-CSF. Furthermore, C15-rhG-CSF by single-dose subcutaneous administration showed better in vivo efficacy than those of both PEG10k-rhG-CSF by single-dose administration and rhG-CSF by multiple doses administration. This study demonstrated the potential of C15-rhG-CSF being developed into a novel drug candidate as well as an efficient process for the development of long-acting protein and peptide drugs.